Generated using: 20Q1

The table below highlights all of the cell lines that are included in the analyses and the types that they are annotated as:

Overview

Expression 2D embedding

Global all cell line expression 2D embedding

Only the top 2000 most variable genes were selected to perform the 2D embedding

tSNE

UMAP

Pediatric cell line expression 2D embedding

Only the top 2000 most variable genes across pediatric cell lines were selected to perform the 2D embedding

tSNE

tSNE with labels

UMAP

UMAP with labels

Dependency 2D embedding

Global (all DepMap cell lines) embedding

Embedding of cell lines in dependency space only using the selective dependencies (LRT > 100, exclude common essentals, exclude non-essentials, exclude genes with NAs):
509, 656 genes

tSNE

UMAP

UMAP - color only peds

tSNE - color tumor types

UMAP - color tumor types

Interactive plot

Pediatric cell line dependency 2D embedding

All selective dependecies (across pediatric and adult solid/brain tumors) across pediatric cell lines were used to perform the 2D embedding

tSNE

tSNE with labels

UMAP

UMAP with labels

Measuring cell line similarity

Here we generate similarity scores between cell lines and then assess the similarity scores.

  • Correlation: calculate the pairwise correlation for all cell lines across the top 2000 or 500 most variable genes (expression or dependency, respectively).

  • Repeated k-means: repeated k-means approach and repeatedly cluster cell lines using kmeans. The similiarity score is the fraction of times that two cell lines cluster with one another.

  • Distance to cluster center in post PCA: run PCA on expression or dependency space and then select the number of PCs that explain the most variabce using the elbow method. For each lineage, set the center of the lineage cluster to be the median of each of the PCs for cell lines in that lineage. Then calculate the average distance of each cell line to the center and plot.

Only tumor types that have >= 3 cell lines are included in this analysis. The black dashed line indicates the median similarity with cell lines not within that tumor type.

Correlations

Repeated kmeans

Distance to center in PCA

Expression

On the top 2000 most variable genes.

Dependency
LRT genes only

Below, we plot the median distance from the cluster center in expression and dependency and then fit a line using the geom_smooth function.

Top 500 genes only

Below, we plot the median distance from the cluster center in expression and dependency and then fit a line using the geom_smooth function.

Session Info

devtools::session_info()
## ─ Session info ───────────────────────────────────────────────────────────────
##  setting  value                       
##  version  R version 3.6.2 (2019-12-12)
##  os       macOS Catalina 10.15.6      
##  system   x86_64, darwin15.6.0        
##  ui       X11                         
##  language (EN)                        
##  collate  en_US.UTF-8                 
##  ctype    en_US.UTF-8                 
##  tz       America/New_York            
##  date     2020-08-18                  
## 
## ─ Packages ───────────────────────────────────────────────────────────────────
##  package         * version    date       lib source        
##  AnnotationDbi     1.48.0     2019-10-29 [1] Bioconductor  
##  ape               5.3        2019-03-17 [1] CRAN (R 3.6.0)
##  askpass           1.1        2019-01-13 [1] CRAN (R 3.6.0)
##  assertthat        0.2.1      2019-03-21 [1] CRAN (R 3.6.0)
##  backports         1.1.6      2020-04-05 [1] CRAN (R 3.6.2)
##  bibtex            0.4.2.2    2020-01-02 [1] CRAN (R 3.6.0)
##  Biobase           2.46.0     2019-10-29 [1] Bioconductor  
##  BiocGenerics      0.32.0     2019-10-29 [1] Bioconductor  
##  BiocManager       1.30.10    2019-11-16 [1] CRAN (R 3.6.0)
##  BiocParallel      1.20.1     2019-12-21 [1] Bioconductor  
##  bit               1.1-15.2   2020-02-10 [1] CRAN (R 3.6.0)
##  bit64             0.9-7      2017-05-08 [1] CRAN (R 3.6.0)
##  bitops            1.0-6      2013-08-17 [1] CRAN (R 3.6.0)
##  blob              1.2.1      2020-01-20 [1] CRAN (R 3.6.0)
##  broom             0.5.5      2020-02-29 [1] CRAN (R 3.6.0)
##  callr             3.4.3      2020-03-28 [1] CRAN (R 3.6.2)
##  caTools           1.18.0     2020-01-17 [1] CRAN (R 3.6.0)
##  cellranger        1.1.0      2016-07-27 [1] CRAN (R 3.6.0)
##  cli               2.0.2      2020-02-28 [1] CRAN (R 3.6.0)
##  cluster           2.1.0      2019-06-19 [1] CRAN (R 3.6.2)
##  clusterProfiler * 3.14.3     2020-01-08 [1] Bioconductor  
##  codetools         0.2-16     2018-12-24 [1] CRAN (R 3.6.2)
##  colorspace        1.4-1      2019-03-18 [1] CRAN (R 3.6.0)
##  cowplot           1.0.0      2019-07-11 [1] CRAN (R 3.6.0)
##  crayon            1.3.4      2017-09-16 [1] CRAN (R 3.6.0)
##  crosstalk         1.1.0.1    2020-03-13 [1] CRAN (R 3.6.0)
##  data.table      * 1.12.8     2019-12-09 [1] CRAN (R 3.6.0)
##  DBI               1.1.0      2019-12-15 [1] CRAN (R 3.6.0)
##  dbplyr            1.4.2      2019-06-17 [1] CRAN (R 3.6.0)
##  desc              1.2.0      2018-05-01 [1] CRAN (R 3.6.0)
##  devtools          2.3.0      2020-04-10 [1] CRAN (R 3.6.2)
##  digest            0.6.25     2020-02-23 [1] CRAN (R 3.6.0)
##  DO.db             2.9        2020-02-13 [1] Bioconductor  
##  DOSE              3.12.0     2019-10-29 [1] Bioconductor  
##  dplyr           * 0.8.5      2020-03-07 [1] CRAN (R 3.6.0)
##  DT              * 0.13       2020-03-23 [1] CRAN (R 3.6.0)
##  ellipsis          0.3.0      2019-09-20 [1] CRAN (R 3.6.0)
##  enrichplot        1.6.1      2019-12-16 [1] Bioconductor  
##  europepmc         0.3        2018-04-20 [1] CRAN (R 3.6.0)
##  evaluate          0.14       2019-05-28 [1] CRAN (R 3.6.0)
##  extrafont       * 0.17       2014-12-08 [1] CRAN (R 3.6.0)
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##  fansi             0.4.1      2020-01-08 [1] CRAN (R 3.6.0)
##  farver            2.0.3      2020-01-16 [1] CRAN (R 3.6.0)
##  fastmatch         1.1-0      2017-01-28 [1] CRAN (R 3.6.0)
##  fgsea             1.12.0     2019-10-29 [1] Bioconductor  
##  fitdistrplus      1.0-14     2019-01-23 [1] CRAN (R 3.6.0)
##  forcats         * 0.5.0      2020-03-01 [1] CRAN (R 3.6.0)
##  fs                1.4.1      2020-04-04 [1] CRAN (R 3.6.2)
##  future            1.16.0     2020-01-16 [1] CRAN (R 3.6.0)
##  future.apply      1.4.0      2020-01-07 [1] CRAN (R 3.6.0)
##  gbRd              0.4-11     2012-10-01 [1] CRAN (R 3.6.0)
##  gdata             2.18.0     2017-06-06 [1] CRAN (R 3.6.0)
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##  ggforce           0.3.1      2019-08-20 [1] CRAN (R 3.6.0)
##  ggplot2         * 3.3.0      2020-03-05 [1] CRAN (R 3.6.0)
##  ggplotify         0.0.5      2020-03-12 [1] CRAN (R 3.6.0)
##  ggpubr          * 0.2.5      2020-02-13 [1] CRAN (R 3.6.0)
##  ggraph            2.0.2      2020-03-17 [1] CRAN (R 3.6.0)
##  ggrepel         * 0.8.2      2020-03-08 [1] CRAN (R 3.6.0)
##  ggridges          0.5.2      2020-01-12 [1] CRAN (R 3.6.0)
##  ggsignif          0.6.0      2019-08-08 [1] CRAN (R 3.6.0)
##  ggthemes        * 4.2.0      2019-05-13 [1] CRAN (R 3.6.0)
##  globals           0.12.5     2019-12-07 [1] CRAN (R 3.6.0)
##  glue              1.4.0      2020-04-03 [1] CRAN (R 3.6.2)
##  GO.db             3.10.0     2020-02-13 [1] Bioconductor  
##  GOSemSim          2.12.1     2020-03-19 [1] Bioconductor  
##  gplots            3.0.3      2020-02-25 [1] CRAN (R 3.6.0)
##  graphlayouts      0.6.0      2020-03-09 [1] CRAN (R 3.6.0)
##  gridExtra       * 2.3        2017-09-09 [1] CRAN (R 3.6.0)
##  gridGraphics      0.5-0      2020-02-25 [1] CRAN (R 3.6.0)
##  gtable            0.3.0      2019-03-25 [1] CRAN (R 3.6.0)
##  gtools            3.8.2      2020-03-31 [1] CRAN (R 3.6.2)
##  haven             2.2.0      2019-11-08 [1] CRAN (R 3.6.0)
##  hms               0.5.3      2020-01-08 [1] CRAN (R 3.6.0)
##  htmltools       * 0.4.0      2019-10-04 [1] CRAN (R 3.6.0)
##  htmlwidgets       1.5.1      2019-10-08 [1] CRAN (R 3.6.0)
##  httr              1.4.1      2019-08-05 [1] CRAN (R 3.6.0)
##  ica               1.0-2      2018-05-24 [1] CRAN (R 3.6.0)
##  igraph            1.2.5      2020-03-19 [1] CRAN (R 3.6.0)
##  IRanges           2.20.2     2020-01-13 [1] Bioconductor  
##  irlba             2.3.3      2019-02-05 [1] CRAN (R 3.6.0)
##  jsonlite          1.6.1      2020-02-02 [1] CRAN (R 3.6.0)
##  KernSmooth        2.23-16    2019-10-15 [1] CRAN (R 3.6.2)
##  knitr             1.28       2020-02-06 [1] CRAN (R 3.6.0)
##  labeling          0.3        2014-08-23 [1] CRAN (R 3.6.0)
##  lattice           0.20-41    2020-04-02 [1] CRAN (R 3.6.2)
##  lazyeval          0.2.2      2019-03-15 [1] CRAN (R 3.6.0)
##  leiden            0.3.3      2020-02-04 [1] CRAN (R 3.6.0)
##  lifecycle         0.2.0      2020-03-06 [1] CRAN (R 3.6.0)
##  limma           * 3.42.2     2020-02-03 [1] Bioconductor  
##  listenv           0.8.0      2019-12-05 [1] CRAN (R 3.6.0)
##  lmtest            0.9-37     2019-04-30 [1] CRAN (R 3.6.0)
##  lsei              1.2-0      2017-10-23 [1] CRAN (R 3.6.0)
##  lubridate         1.7.8      2020-04-06 [1] CRAN (R 3.6.2)
##  magrittr        * 1.5        2014-11-22 [1] CRAN (R 3.6.0)
##  MASS              7.3-51.5   2019-12-20 [1] CRAN (R 3.6.0)
##  Matrix            1.2-18     2019-11-27 [1] CRAN (R 3.6.2)
##  matrixStats     * 0.56.0     2020-03-13 [1] CRAN (R 3.6.0)
##  memoise           1.1.0      2017-04-21 [1] CRAN (R 3.6.0)
##  metap             1.3        2020-01-23 [1] CRAN (R 3.6.0)
##  mgcv              1.8-31     2019-11-09 [1] CRAN (R 3.6.2)
##  mnormt            1.5-6      2020-02-03 [1] CRAN (R 3.6.0)
##  modelr            0.1.6      2020-02-22 [1] CRAN (R 3.6.0)
##  multcomp          1.4-13     2020-04-08 [1] CRAN (R 3.6.2)
##  multtest          2.42.0     2019-10-29 [1] Bioconductor  
##  munsell           0.5.0      2018-06-12 [1] CRAN (R 3.6.0)
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##  mvtnorm           1.1-0      2020-02-24 [1] CRAN (R 3.6.0)
##  nlme              3.1-145    2020-03-04 [1] CRAN (R 3.6.0)
##  npsurv            0.4-0      2017-10-14 [1] CRAN (R 3.6.0)
##  numDeriv          2016.8-1.1 2019-06-06 [1] CRAN (R 3.6.0)
##  openssl           1.4.1      2019-07-18 [1] CRAN (R 3.6.0)
##  patchwork         1.0.0      2019-12-01 [1] CRAN (R 3.6.0)
##  pbapply         * 1.4-2      2019-08-31 [1] CRAN (R 3.6.0)
##  pheatmap        * 1.0.12     2019-01-04 [1] CRAN (R 3.6.0)
##  pillar            1.4.3      2019-12-20 [1] CRAN (R 3.6.0)
##  pkgbuild          1.0.6      2019-10-09 [1] CRAN (R 3.6.0)
##  pkgconfig         2.0.3      2019-09-22 [1] CRAN (R 3.6.0)
##  pkgload           1.0.2      2018-10-29 [1] CRAN (R 3.6.0)
##  plotly          * 4.9.2.1    2020-04-04 [1] CRAN (R 3.6.2)
##  plotrix           3.7-7      2019-12-05 [1] CRAN (R 3.6.0)
##  plyr            * 1.8.6      2020-03-03 [1] CRAN (R 3.6.0)
##  png               0.1-7      2013-12-03 [1] CRAN (R 3.6.0)
##  polyclip          1.10-0     2019-03-14 [1] CRAN (R 3.6.0)
##  prettyunits       1.1.1      2020-01-24 [1] CRAN (R 3.6.2)
##  processx          3.4.2      2020-02-09 [1] CRAN (R 3.6.0)
##  progress          1.2.2      2019-05-16 [1] CRAN (R 3.6.0)
##  ps                1.3.2      2020-02-13 [1] CRAN (R 3.6.0)
##  purrr           * 0.3.3      2019-10-18 [1] CRAN (R 3.6.0)
##  qvalue            2.18.0     2019-10-29 [1] Bioconductor  
##  R6                2.4.1      2019-11-12 [1] CRAN (R 3.6.0)
##  RANN              2.6.1      2019-01-08 [1] CRAN (R 3.6.0)
##  RColorBrewer    * 1.1-2      2014-12-07 [1] CRAN (R 3.6.0)
##  Rcpp              1.0.4.6    2020-04-09 [1] CRAN (R 3.6.2)
##  RcppAnnoy         0.0.16     2020-03-08 [1] CRAN (R 3.6.0)
##  Rdpack            0.11-1     2019-12-14 [1] CRAN (R 3.6.0)
##  readr           * 1.3.1      2018-12-21 [1] CRAN (R 3.6.0)
##  readxl          * 1.3.1      2019-03-13 [1] CRAN (R 3.6.0)
##  remotes           2.1.1      2020-02-15 [1] CRAN (R 3.6.0)
##  reprex            0.3.0      2019-05-16 [1] CRAN (R 3.6.0)
##  reshape2          1.4.4      2020-04-09 [1] CRAN (R 3.6.2)
##  reticulate        1.15       2020-04-02 [1] CRAN (R 3.6.2)
##  rlang             0.4.5      2020-03-01 [1] CRAN (R 3.6.0)
##  rmarkdown         2.1        2020-01-20 [1] CRAN (R 3.6.0)
##  ROCR              1.0-7      2015-03-26 [1] CRAN (R 3.6.0)
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##  RSpectra          0.16-0     2019-12-01 [1] CRAN (R 3.6.0)
##  RSQLite           2.2.0      2020-01-07 [1] CRAN (R 3.6.0)
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##  rsvd              1.0.3      2020-02-17 [1] CRAN (R 3.6.0)
##  Rtsne           * 0.15       2018-11-10 [1] CRAN (R 3.6.0)
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##  rvcheck           0.1.8      2020-03-01 [1] CRAN (R 3.6.0)
##  rvest             0.3.5      2019-11-08 [1] CRAN (R 3.6.0)
##  S4Vectors         0.24.4     2020-04-09 [1] Bioconductor  
##  sandwich          2.5-1      2019-04-06 [1] CRAN (R 3.6.0)
##  scales          * 1.1.0      2019-11-18 [1] CRAN (R 3.6.0)
##  sctransform       0.2.1      2019-12-17 [1] CRAN (R 3.6.0)
##  sessioninfo       1.1.1      2018-11-05 [1] CRAN (R 3.6.0)
##  Seurat          * 3.1.4      2020-02-26 [1] CRAN (R 3.6.0)
##  sn                1.6-1      2020-04-01 [1] CRAN (R 3.6.2)
##  stringi           1.4.6      2020-02-17 [1] CRAN (R 3.6.0)
##  stringr         * 1.4.0      2019-02-10 [1] CRAN (R 3.6.0)
##  survival          3.1-12     2020-04-10 [1] CRAN (R 3.6.2)
##  testthat          2.3.2      2020-03-02 [1] CRAN (R 3.6.0)
##  TFisher           0.2.0      2018-03-21 [1] CRAN (R 3.6.0)
##  TH.data           1.0-10     2019-01-21 [1] CRAN (R 3.6.0)
##  tibble          * 3.0.0      2020-03-30 [1] CRAN (R 3.6.2)
##  tidygraph         1.1.2      2019-02-18 [1] CRAN (R 3.6.0)
##  tidyr           * 1.0.2      2020-01-24 [1] CRAN (R 3.6.2)
##  tidyselect        1.0.0      2020-01-27 [1] CRAN (R 3.6.2)
##  tidyverse       * 1.3.0      2019-11-21 [1] CRAN (R 3.6.0)
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##  tweenr            1.0.1      2018-12-14 [1] CRAN (R 3.6.0)
##  umap            * 0.2.5.0    2020-03-09 [1] CRAN (R 3.6.0)
##  urltools          1.7.3      2019-04-14 [1] CRAN (R 3.6.0)
##  usethis           1.6.0      2020-04-09 [1] CRAN (R 3.6.2)
##  uwot              0.1.8      2020-03-16 [1] CRAN (R 3.6.0)
##  vctrs             0.2.4      2020-03-10 [1] CRAN (R 3.6.0)
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##  withr             2.1.2      2018-03-15 [1] CRAN (R 3.6.0)
##  xfun              0.13       2020-04-13 [1] CRAN (R 3.6.2)
##  xml2              1.3.1      2020-04-09 [1] CRAN (R 3.6.2)
##  yaml              2.2.1      2020-02-01 [1] CRAN (R 3.6.0)
##  zoo               1.8-7      2020-01-10 [1] CRAN (R 3.6.0)
## 
## [1] /Library/Frameworks/R.framework/Versions/3.6/Resources/library